Job ID = 1294670 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,164,185 reads read : 11,164,185 reads written : 11,164,185 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:49 11164185 reads; of these: 11164185 (100.00%) were unpaired; of these: 352592 (3.16%) aligned 0 times 9467376 (84.80%) aligned exactly 1 time 1344217 (12.04%) aligned >1 times 96.84% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1497718 / 10811593 = 0.1385 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 09:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 09:42:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:42:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 09:42:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:42:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 09:42:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:42:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:43:02: 1000000 INFO @ Mon, 03 Jun 2019 09:43:05: 1000000 INFO @ Mon, 03 Jun 2019 09:43:05: 1000000 INFO @ Mon, 03 Jun 2019 09:43:09: 2000000 INFO @ Mon, 03 Jun 2019 09:43:15: 2000000 INFO @ Mon, 03 Jun 2019 09:43:16: 2000000 INFO @ Mon, 03 Jun 2019 09:43:16: 3000000 INFO @ Mon, 03 Jun 2019 09:43:24: 4000000 INFO @ Mon, 03 Jun 2019 09:43:26: 3000000 INFO @ Mon, 03 Jun 2019 09:43:26: 3000000 INFO @ Mon, 03 Jun 2019 09:43:31: 5000000 INFO @ Mon, 03 Jun 2019 09:43:35: 4000000 INFO @ Mon, 03 Jun 2019 09:43:35: 4000000 INFO @ Mon, 03 Jun 2019 09:43:38: 6000000 INFO @ Mon, 03 Jun 2019 09:43:45: 5000000 INFO @ Mon, 03 Jun 2019 09:43:45: 5000000 INFO @ Mon, 03 Jun 2019 09:43:45: 7000000 INFO @ Mon, 03 Jun 2019 09:43:52: 8000000 INFO @ Mon, 03 Jun 2019 09:43:54: 6000000 INFO @ Mon, 03 Jun 2019 09:43:55: 6000000 INFO @ Mon, 03 Jun 2019 09:43:59: 9000000 INFO @ Mon, 03 Jun 2019 09:44:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:44:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:44:02: #1 total tags in treatment: 9313875 INFO @ Mon, 03 Jun 2019 09:44:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:44:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:44:02: #1 tags after filtering in treatment: 9313875 INFO @ Mon, 03 Jun 2019 09:44:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:44:02: #1 finished! INFO @ Mon, 03 Jun 2019 09:44:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:44:04: 7000000 INFO @ Mon, 03 Jun 2019 09:44:04: #2 number of paired peaks: 9580 INFO @ Mon, 03 Jun 2019 09:44:04: start model_add_line... INFO @ Mon, 03 Jun 2019 09:44:04: start X-correlation... INFO @ Mon, 03 Jun 2019 09:44:04: end of X-cor INFO @ Mon, 03 Jun 2019 09:44:04: #2 finished! INFO @ Mon, 03 Jun 2019 09:44:04: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 09:44:04: #2 alternative fragment length(s) may be 4,212 bps INFO @ Mon, 03 Jun 2019 09:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.05_model.r INFO @ Mon, 03 Jun 2019 09:44:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:44:04: 7000000 INFO @ Mon, 03 Jun 2019 09:44:13: 8000000 INFO @ Mon, 03 Jun 2019 09:44:14: 8000000 INFO @ Mon, 03 Jun 2019 09:44:23: 9000000 INFO @ Mon, 03 Jun 2019 09:44:24: 9000000 INFO @ Mon, 03 Jun 2019 09:44:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:44:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:44:26: #1 total tags in treatment: 9313875 INFO @ Mon, 03 Jun 2019 09:44:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:44:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:44:26: #1 tags after filtering in treatment: 9313875 INFO @ Mon, 03 Jun 2019 09:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:44:26: #1 finished! INFO @ Mon, 03 Jun 2019 09:44:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:44:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:44:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:44:27: #1 total tags in treatment: 9313875 INFO @ Mon, 03 Jun 2019 09:44:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:44:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:44:27: #1 tags after filtering in treatment: 9313875 INFO @ Mon, 03 Jun 2019 09:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:44:27: #1 finished! INFO @ Mon, 03 Jun 2019 09:44:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:44:28: #2 number of paired peaks: 9580 INFO @ Mon, 03 Jun 2019 09:44:28: start model_add_line... INFO @ Mon, 03 Jun 2019 09:44:28: start X-correlation... INFO @ Mon, 03 Jun 2019 09:44:28: end of X-cor INFO @ Mon, 03 Jun 2019 09:44:28: #2 finished! INFO @ Mon, 03 Jun 2019 09:44:28: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 09:44:28: #2 alternative fragment length(s) may be 4,212 bps INFO @ Mon, 03 Jun 2019 09:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.20_model.r INFO @ Mon, 03 Jun 2019 09:44:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:44:29: #2 number of paired peaks: 9580 INFO @ Mon, 03 Jun 2019 09:44:29: start model_add_line... INFO @ Mon, 03 Jun 2019 09:44:29: start X-correlation... INFO @ Mon, 03 Jun 2019 09:44:29: end of X-cor INFO @ Mon, 03 Jun 2019 09:44:29: #2 finished! INFO @ Mon, 03 Jun 2019 09:44:29: #2 predicted fragment length is 212 bps INFO @ Mon, 03 Jun 2019 09:44:29: #2 alternative fragment length(s) may be 4,212 bps INFO @ Mon, 03 Jun 2019 09:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.10_model.r INFO @ Mon, 03 Jun 2019 09:44:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:44:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.05_summits.bed INFO @ Mon, 03 Jun 2019 09:44:50: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8429 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:44:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:45:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.20_summits.bed INFO @ Mon, 03 Jun 2019 09:45:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2144 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:45:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:45:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287815/SRX287815.10_summits.bed INFO @ Mon, 03 Jun 2019 09:45:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5246 records, 4 fields): 105 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。